RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4233
(303 letters)
>gnl|CDD|187579 cd05271, NDUFA9_like_SDR_a, NADH dehydrogenase (ubiquinone) 1 alpha
subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical
(a) SDRs. This subgroup of extended SDR-like proteins
are atypical SDRs. They have a glycine-rich
NAD(P)-binding motif similar to the typical SDRs,
GXXGXXG, and have the YXXXK active site motif (though
not the other residues of the SDR tetrad). Members
identified include NDUFA9 (mitochondrial) and putative
nucleoside-diphosphate-sugar epimerase. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 273
Score = 316 bits (811), Expect = e-108
Identities = 126/286 (44%), Positives = 172/286 (60%), Gaps = 19/286 (6%)
Query: 19 VVATVFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRND 78
+V TVFGA+G++G Y+ N+L K+GSQ+I+PYR Y R L + GDLGQVLF + R+D
Sbjct: 1 MVVTVFGATGFIGRYVVNRLAKRGSQVIVPYRCEAYARRLL-VMGDLGQVLFVEFDLRDD 59
Query: 79 DEIRKAIKYSNVVINLIGREFATKNFTIADANVEIPARLARLSKEMGVEKFIHISALNAD 138
+ IRKA++ S+VVINL+GR + TKNF+ D +VE P RLA+ +KE GVE+ IHISAL AD
Sbjct: 60 ESIRKALEGSDVVINLVGRLYETKNFSFEDVHVEGPERLAKAAKEAGVERLIHISALGAD 119
Query: 139 PNPPTYYISGGSQFYRTKYQGEKEVLREFPEATIFRPSDMYGSGDKFLRYYGHMWRHVFR 198
N P+ Y+ R+K +GE+ V FPEATI RPS ++G D+FL + + F
Sbjct: 120 ANSPSKYL-------RSKAEGEEAVREAFPEATIVRPSVVFGREDRFLNRFAKLLA--FL 170
Query: 199 KLAVYKKGEETIKQPVYVGDVAAAIVAACKDPDAAGKIYQAVGPKRYLLSELLDWFHVVM 258
G +T QPVYVGDVA AI A KDP+ GK Y+ VGPK Y L+EL++
Sbjct: 171 PFPPLIGGGQTKFQPVYVGDVAEAIARALKDPETEGKTYELVGPKVYTLAELVELLR--- 227
Query: 259 KKGEPDYGYYRYDLRYDP-VMPLKLFINGLFPGYPMGHLTPERVER 303
G + + P + + L P LT +++ER
Sbjct: 228 -----RLGGRKRRVLPLPLWLARLIARVKLLLLLPEPPLTRDQLER 268
>gnl|CDD|187537 cd05226, SDR_e_a, Extended (e) and atypical (a) SDRs. Extended or
atypical short-chain dehydrogenases/reductases (SDRs,
aka tyrosine-dependent oxidoreductases) are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. Atypical SDRs generally
lack the catalytic residues characteristic of the SDRs,
and their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 176
Score = 95.9 bits (239), Expect = 4e-24
Identities = 45/168 (26%), Positives = 74/168 (44%), Gaps = 10/168 (5%)
Query: 21 ATVFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCG-DLGQVLFQPYHPRNDD 79
+ GA+G++G L +L +QG ++ + R RL D V R+ D
Sbjct: 1 ILILGATGFIGRALARELLEQGHEVTLLVR------NTKRLSKEDQEPVAVVEGDLRDLD 54
Query: 80 EIRKAIKYSNVVINLIGREFATKNFTIADANVEIPARLARLSKEMGVEKFIHISALNADP 139
+ A++ +VVI+L G T++F + +VE + +KE GV+ FI IS+L A
Sbjct: 55 SLSDAVQGVDVVIHLAGAPRDTRDFC--EVDVEGTRNVLEAAKEAGVKHFIFISSLGAYG 112
Query: 140 NPPTYYISGGSQFY-RTKYQGEKEVLREFPEATIFRPSDMYGSGDKFL 186
+ S Y K + E + TI RP +YG + +
Sbjct: 113 DLHEETEPSPSSPYLAVKAKTEAVLREASLPYTIVRPGVIYGDLARAI 160
>gnl|CDD|216461 pfam01370, Epimerase, NAD dependent epimerase/dehydratase family.
This family of proteins utilise NAD as a cofactor. The
proteins in this family use nucleotide-sugar substrates
for a variety of chemical reactions.
Length = 233
Score = 78.5 bits (194), Expect = 4e-17
Identities = 54/245 (22%), Positives = 98/245 (40%), Gaps = 43/245 (17%)
Query: 21 ATVFGASGYMGSYLCNKLGKQGSQIIIPYRG----NFYDVRDLRLCGDLGQVLFQPYHPR 76
V G +G++GS+L +L ++G ++I+ R + R GDL
Sbjct: 1 ILVTGGTGFIGSHLVRRLLQEGYEVIVLGRRRRSESLNTGRIRFHEGDL----------T 50
Query: 77 NDDEIRKAIKYS--NVVINLIGREFATKNFT----IADANVEIPARLARLSKEMGVEKFI 130
+ D + + + + VI+L + +F ANV RL ++ GV++F+
Sbjct: 51 DPDALERLLAEVQPDAVIHLAAQSGVGASFEDPADFIRANVLGTLRLLEAARRAGVKRFV 110
Query: 131 HISALNADPNPPTYYISGGSQFY------RTKYQGEKEVLREFPE----ATIFRPSDMYG 180
S+ + I+ + K E+ V A I R ++YG
Sbjct: 111 FASSSEVYGDVADPPITEDTPLGPLSPYAAAKLAAERLVEAYARAYGLRAVILRLFNVYG 170
Query: 181 SGDKFLRYYGHMWRHVFRKLAVYKKGEETIKQP--------VYVGDVAAAIVAACKDPDA 232
G+ + H+ + R++ +G+ + +YV DVA AI+ A + PD
Sbjct: 171 PGN-PDPFVTHVIPALIRRI---LEGKPILLLGDGTQRRDFLYVDDVARAILLALEHPD- 225
Query: 233 AGKIY 237
G+IY
Sbjct: 226 GGEIY 230
>gnl|CDD|223528 COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases [Cell
envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 314
Score = 73.8 bits (181), Expect = 4e-15
Identities = 60/285 (21%), Positives = 96/285 (33%), Gaps = 34/285 (11%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRNDDEIR 82
V G +G++GS+L +L G + D L L V F + D +
Sbjct: 5 VTGGAGFIGSHLVERLLAAGHDVRG------LDRLRDGLDPLLSGVEFVVLDLTDRDLVD 58
Query: 83 KAIKYSN-VVINLIGR-----EFATKNFTIADANVEIPARLARLSKEMGVEKFIHISA-- 134
+ K VI+L + A+ D NV+ L ++ GV++F+ S+
Sbjct: 59 ELAKGVPDAVIHLAAQSSVPDSNASDPAEFLDVNVDGTLNLLEAARAAGVKRFVFASSVS 118
Query: 135 -----LNADPNPPTYYISGGSQFY-RTKYQGEKEVLREFP----EATIFRPSDMYGSGDK 184
P Y +K E+ + I RP ++YG GDK
Sbjct: 119 VVYGDPPPLPIDEDLGPPRPLNPYGVSKLAAEQLLRAYARLYGLPVVILRPFNVYGPGDK 178
Query: 185 FLRYYGHMWRHVFRKLA------VYKKGEETIKQPVYVGDVAAAIVAACKDPDAAGKIYQ 238
+ R+L V + VYV DVA A++ A ++PD G ++
Sbjct: 179 P-DLSSGVVSAFIRQLLKGEPIIVIGGDGSQTRDFVYVDDVADALLLALENPD--GGVFN 235
Query: 239 AVGPKR-YLLSELLDWFHVVMKKGEPDYGYYRYDLRYDPVMPLKL 282
+ EL + + P Y R D L
Sbjct: 236 IGSGTAEITVRELAEAVAEAVGSKAPLIVYIPLGRRGDLREGKLL 280
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 72.7 bits (179), Expect = 7e-15
Identities = 59/257 (22%), Positives = 90/257 (35%), Gaps = 84/257 (32%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRNDDEIR 82
+ GA+G +G+ L + ++I R D+ D D +
Sbjct: 5 ITGANGQLGTELR-RALPGEFEVIATDRAEL-DITD-------------------PDAVL 43
Query: 83 KAIKYSN--VVINLIGREFATKNFTIAD-----------ANVEIPARLARLSKEMGVEKF 129
+ I+ + VVIN +T D N LAR + E+G +
Sbjct: 44 EVIRETRPDVVINAAA-------YTAVDKAESEPELAFAVNATGAENLARAAAEVGA-RL 95
Query: 130 IHISALNADPNPPTYYISGG--SQFY-------------RTKYQGEKEVLREFPEATIFR 174
+HIS T Y+ G Y R+K GE+ V P I R
Sbjct: 96 VHIS---------TDYVFDGEKGGPYKETDTPNPLNVYGRSKLAGEEAVRAAGPRHLILR 146
Query: 175 PSDMYGS-GDKFLRYYGHMWRHVFRKLAVYKKGEET------IKQPVYVGDVAAAIVAAC 227
S +YG G+ F++ M R LA K+G+E P Y D+A AI+
Sbjct: 147 TSWVYGEYGNNFVKT---MLR-----LA--KEGKELKVVDDQYGSPTYTEDLADAILELL 196
Query: 228 KDPDAAGKIYQAVGPKR 244
+ + G +Y V
Sbjct: 197 -EKEKEGGVYHLVNSGE 212
>gnl|CDD|187564 cd05254, dTDP_HR_like_SDR_e, dTDP-6-deoxy-L-lyxo-4-hexulose
reductase and related proteins, extended (e) SDRs.
dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended
SDR, synthesizes dTDP-L-rhamnose from
alpha-D-glucose-1-phosphate, providing the precursor of
L-rhamnose, an essential cell wall component of many
pathogenic bacteria. This subgroup has the
characteristic active site tetrad and NADP-binding
motif. This subgroup also contains human MAT2B, the
regulatory subunit of methionine adenosyltransferase
(MAT); MAT catalyzes S-adenosylmethionine synthesis. The
human gene encoding MAT2B encodes two major splicing
variants which are induced in human cell liver cancer
and regulate HuR, an mRNA-binding protein which
stabilizes the mRNA of several cyclins, to affect cell
proliferation. Both MAT2B variants include this extended
SDR domain. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 280
Score = 72.3 bits (178), Expect = 1e-14
Identities = 64/251 (25%), Positives = 93/251 (37%), Gaps = 65/251 (25%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRNDDEIR 82
+ GA+G +G L L ++G ++I R DL + D +
Sbjct: 4 ITGATGMLGRALVRLLKERGYEVIGTGRSRASL-----FKLDL----------TDPDAVE 48
Query: 83 KAI-KYS-NVVINLIG------RE-FATKNFTIADANVEIPARLARLSKEMGVEKFIHIS 133
+AI Y +V+IN E + + NV P LAR +KE+G + IHIS
Sbjct: 49 EAIRDYKPDVIINCAAYTRVDKCESDPELAYRV---NVLAPENLARAAKEVGA-RLIHIS 104
Query: 134 ALNAD---------------PNPPTYYISGGSQFYRTKYQGEKEVLREFPEATIFRPSDM 178
D PNP Y G ++K GE VL P I R S +
Sbjct: 105 T---DYVFDGKKGPYKEEDAPNPLNVY---G----KSKLLGEVAVLNANPRYLILRTSWL 154
Query: 179 YGS---GDKFLRYYGHMWRHV--FRKLAVYKKGEETIKQPVYVGDVAAAIVAACKDPDAA 233
YG G+ F+ + M R +++ V I P Y D+A AI+ +
Sbjct: 155 YGELKNGENFVEW---MLRLAAERKEVNVVHDQ---IGSPTYAADLADAILELIERNSLT 208
Query: 234 GKIYQAVGPKR 244
G IY
Sbjct: 209 G-IYHLSNSGP 218
>gnl|CDD|187554 cd05243, SDR_a5, atypical (a) SDRs, subgroup 5. This subgroup
contains atypical SDRs, some of which are identified as
putative NAD(P)-dependent epimerases, one as a putative
NAD-dependent epimerase/dehydratase. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
have a glycine-rich NAD(P)-binding motif that is very
similar to the extended SDRs, GXXGXXG, and binds NADP.
Generally, this subgroup has poor conservation of the
active site tetrad; however, individual sequences do
contain matches to the YXXXK active site motif, the
upstream Ser, and there is a highly conserved Asp in
place of the usual active site Asn throughout the
subgroup. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 203
Score = 70.0 bits (172), Expect = 3e-14
Identities = 46/233 (19%), Positives = 88/233 (37%), Gaps = 45/233 (19%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIII----PYRGNFYDVRDLRLC-GDLGQVLFQPYHPRN 77
V GA+G +G ++ +L +G Q+ P + + + GDL +
Sbjct: 4 VVGATGKVGRHVVRELLDRGYQVRALVRDPSQAEKLEAAGAEVVVGDL----------TD 53
Query: 78 DDEIRKAIKYSNVVINLIG--REFATKNFTI-ADANVEIPARLARLSKEMGVEKFIHISA 134
+ + A++ + VI+ G + + + D N+ L +K+ GV++F+ +S+
Sbjct: 54 AESLAAALEGIDAVISAAGSGGKGGPRTEAVDYDGNI----NLIDAAKKAGVKRFVLVSS 109
Query: 135 LNADPNPPTYYISGGSQFYRTKYQGEKEVLREFPEATIFRP----SDMYGSGDKFLRYYG 190
+ AD + + K + E + + TI RP D G+G
Sbjct: 110 IGADKPSH--PLEALGPYLDAKRKAEDYLRASGLDYTIVRPGGLTDDPAGTG-------- 159
Query: 191 HMWRHVFRKLAVYKKGEETIKQPVYVGDVAAAIVAACKDPDAAGKIYQAVGPK 243
++ + G P+ DVA + A P A GK ++ G
Sbjct: 160 --------RVVLGGDGTRLDG-PISRADVAEVLAEALDTPAAIGKTFELGGGD 203
>gnl|CDD|187543 cd05232, UDP_G4E_4_SDR_e, UDP-glucose 4 epimerase, subgroup 4,
extended (e) SDRs. UDP-glucose 4 epimerase (aka
UDP-galactose-4-epimerase), is a homodimeric extended
SDR. It catalyzes the NAD-dependent conversion of
UDP-galactose to UDP-glucose, the final step in Leloir
galactose synthesis. This subgroup is comprised of
bacterial proteins, and includes the Staphylococcus
aureus capsular polysaccharide Cap5N, which may have a
role in the synthesis of UDP-N-acetyl-d-fucosamine. This
subgroup has the characteristic active site tetrad and
NAD-binding motif of the extended SDRs. Extended SDRs
are distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 303
Score = 66.2 bits (162), Expect = 2e-12
Identities = 57/256 (22%), Positives = 96/256 (37%), Gaps = 48/256 (18%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRNDDEIR 82
V GA+G++G L +KL +G ++ I R + VL + P D
Sbjct: 4 VTGANGFIGRALVDKLLSRGEEVRIAVR--------NAENAEPSVVLAE--LPDIDSFTD 53
Query: 83 KAIKYSNVVINLIGREFATKNFTIA------DANVEIPARLARLSKEMGVEKFIHISALN 136
+ V++L R + N E+ RLAR + GV++F+ +S++
Sbjct: 54 -LFLGVDAVVHLAARVHVMNDQGADPLSDYRKVNTELTRRLARAAARQGVKRFVFLSSVK 112
Query: 137 AD--------------PNPPTYYISGGSQFYRTKYQGEKEVLREFP----EATIFRPSDM 178
+ P P Y G R+K + E+ +L E I RP +
Sbjct: 113 VNGEGTVGAPFDETDPPAPQDAY--G-----RSKLEAERALLELGASDGMEVVILRPPMV 165
Query: 179 YGSGDK--FLRYYGHMWRHVFRKLAVYKKGEETIKQPVYVGDVAAAIVAACKDPDAAGKI 236
YG G + F R + R + R L + + + V + ++ AI P AA
Sbjct: 166 YGPGVRGNFAR----LMRLIDRGLPLPPGAVKNRRSLVSLDNLVDAIYLCISLPKAANGT 221
Query: 237 YQAVGPKRYLLSELLD 252
+ +EL+D
Sbjct: 222 FLVSDGPPVSTAELVD 237
>gnl|CDD|187575 cd05265, SDR_a1, atypical (a) SDRs, subgroup 1. Atypical SDRs in
this subgroup are poorly defined and have been
identified putatively as isoflavones reductase, sugar
dehydratase, mRNA binding protein etc. Atypical SDRs are
distinct from classical SDRs. Members of this subgroup
retain the canonical active site triad (though not the
upstream Asn found in most SDRs) but have an unusual
putative glycine-rich NAD(P)-binding motif, GGXXXXG, in
the usual location. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 250
Score = 65.0 bits (159), Expect = 2e-12
Identities = 51/248 (20%), Positives = 94/248 (37%), Gaps = 40/248 (16%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRNDDEIR 82
+ G + ++G L +L G + + RG L + ++ +E+
Sbjct: 5 IIGGTRFIGKALVEELLAAGHDVTVFNRGR----TKPDLPEGVEHIVGDRNDRDALEELL 60
Query: 83 KAIKYSNVVINLIGREFATKNFTIADANVEIPARLARLSKEMGVEKFIHISALNA----- 137
+ +VV++ I +T R K V+++I IS+ +
Sbjct: 61 GGEDF-DVVVDTIA-------YTPRQV-----ERALDAFK-GRVKQYIFISSASVYLKPG 106
Query: 138 ----DPNP--PTYYISGGSQFYRT--KYQGEKEVLRE--FPEATIFRPSDMYGSGDKFLR 187
+ P + + K E ++ FP TI RP +YG GD R
Sbjct: 107 RVITESTPLREPDAVGLSDPWDYGRGKRAAEDVLIEAAAFP-YTIVRPPYIYGPGDYTGR 165
Query: 188 ---YYGHMWRHVFRKLAVYKKGEETIKQPVYVGDVAAAIVAACKDPDAAGKIYQAVGPKR 244
++ + R R + V G ++ Q ++V D+A A++ A +P A G I+ G +
Sbjct: 166 LAYFFDRLARG--RPILVPGDGH-SLVQFIHVKDLARALLGAAGNPKAIGGIFNITGDEA 222
Query: 245 YLLSELLD 252
ELL+
Sbjct: 223 VTWDELLE 230
>gnl|CDD|187539 cd05228, AR_FR_like_1_SDR_e, uncharacterized subgroup of aldehyde
reductase and flavonoid reductase related proteins,
extended (e) SDRs. This subgroup contains proteins of
unknown function related to aldehyde reductase and
flavonoid reductase of the extended SDR-type. Aldehyde
reductase I (aka carbonyl reductase) is an NADP-binding
SDR; it has an NADP-binding motif consensus that is
slightly different from the canonical SDR form and lacks
the Asn of the extended SDR active site tetrad. Aldehyde
reductase I catalyzes the NADP-dependent reduction of
ethyl 4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 318
Score = 65.0 bits (159), Expect = 4e-12
Identities = 59/257 (22%), Positives = 83/257 (32%), Gaps = 64/257 (24%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHP------- 75
V GA+G++GS L L QG Y VR L + P
Sbjct: 3 VTGATGFLGSNLVRALLAQG-----------YRVRALVR--SGSDAVLLDGLPVEVVEGD 49
Query: 76 -RNDDEIRKAIKYSNVVINLIG--REFATKNFTIADANVEIPARLARLSKEMGVEKFIHI 132
+ + A+K + V +L +A + NVE + + E GV + +H
Sbjct: 50 LTDAASLAAAMKGCDRVFHLAAFTSLWAKDRKELYRTNVEGTRNVLDAALEAGVRRVVHT 109
Query: 133 S---ALNADPNPP---TYYISGGSQF---YRTKYQGEKEVLREFPE---ATIFRPSDMYG 180
S AL P+ T + YR+K E EVL E I PS ++G
Sbjct: 110 SSIAALGGPPDGRIDETTPWNERPFPNDYYRSKLLAELEVLEAAAEGLDVVIVNPSAVFG 169
Query: 181 SGDKFLRYYGHMWRHVFRKLAVYKKGEETIKQP---------VYVGDVAAAIVAACKDPD 231
GD+ L K P V V DVA +AA +
Sbjct: 170 PGDE------GPTSTGLDVLDYLNG-----KLPAYPPGGTSFVDVRDVAEGHIAAMEKGR 218
Query: 232 AAGKIYQAVGPKRYLLS 248
RY+L
Sbjct: 219 RGE---------RYILG 226
>gnl|CDD|223774 COG0702, COG0702, Predicted nucleoside-diphosphate-sugar epimerases
[Cell envelope biogenesis, outer membrane / Carbohydrate
transport and metabolism].
Length = 275
Score = 64.9 bits (158), Expect = 4e-12
Identities = 46/238 (19%), Positives = 77/238 (32%), Gaps = 38/238 (15%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRNDDEIR 82
V GA+G++G + +L +G ++ VR+ L + ++R
Sbjct: 5 VTGATGFVGGAVVRELLARGHEVRA-------AVRNPEAAAALAGGV-----EVVLGDLR 52
Query: 83 KAIKYSNVVINLIGREFATKNFTIADANVEIPARLAR---LSKEMGVEKFIHISALNADP 139
+ G + +DA + + GV+ + +S L AD
Sbjct: 53 DPKSLVAGAKGVDGVLLISGLLDGSDAFRAVQVTAVVRAAEAAGAGVKHGVSLSVLGADA 112
Query: 140 NPPTYYISGGSQFYRTKYQGEKEVLREFPEATIFRPSDMYGSGDKFLRYYGHMWRHVFRK 199
P+ R K E + T R + Y F +
Sbjct: 113 ASPSALA-------RAKAAVEAALRSSGIPYTTLRRAAFYLG-----------AGAAFIE 154
Query: 200 LAVYKKGEETIK-----QPVYVGDVAAAIVAACKDPDAAGKIYQAVGPKRYLLSELLD 252
A + P+ V DVA A+ AA P AG+ Y+ GP+ L+EL
Sbjct: 155 AAEAAGLPVIPRGIGRLSPIAVDDVAEALAAALDAPATAGRTYELAGPEALTLAELAS 212
>gnl|CDD|187560 cd05250, CC3_like_SDR_a, CC3(TIP30)-like, atypical (a) SDRs.
Atypical SDRs in this subgroup include CC3 (also known
as TIP30) which is implicated in tumor suppression.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine rich NAD(P)-binding
motif that resembles the extended SDRs, and have an
active site triad of the SDRs (YXXXK and upstream Ser),
although the upstream Asn of the usual SDR active site
is substituted with Asp. For CC3, the Tyr of the triad
is displaced compared to the usual SDRs and the protein
is monomeric, both these observations suggest that the
usual SDR catalytic activity is not present. NADP
appears to serve an important role as a ligand, and may
be important in the interaction with other
macromolecules. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 214
Score = 58.8 bits (143), Expect = 2e-10
Identities = 51/230 (22%), Positives = 92/230 (40%), Gaps = 44/230 (19%)
Query: 21 ATVFGASGYMGSYLCNKLGKQG--SQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPR-- 76
A V GA+G +G +L +L K S++ R R ++ F +
Sbjct: 3 ALVLGATGLVGKHLLRELLKSPYYSKVTAIVR---------R------KLTFPEAKEKLV 47
Query: 77 ----NDDEI-RKAIKYSN--VVINLIG----REFATKNFTIADANVEIPARLARLSKEMG 125
+ + + + N V +G + + +NF D + +LA+L+K G
Sbjct: 48 QIVVDFERLDEYLEAFQNPDVGFCCLGTTRKKAGSQENFRKVD--HDYVLKLAKLAKAAG 105
Query: 126 VEKFIHISALNADPNPPTYYISGGSQFYRTKYQGEKEVLRE-FPEATIFRPSDMYGSGDK 184
V+ F+ +S+L ADP Y+ + K + E+++ + F TIFRP + G +
Sbjct: 106 VQHFLLVSSLGADPKSSFLYL-------KVKGEVERDLQKLGFERLTIFRPGLLLGERQE 158
Query: 185 FLRYYGHMWRHVFRKLAVYKKGEETIKQPVYVGDVAAAIVAACKDPDAAG 234
R + + + R L+ K P+ VA A+V A +
Sbjct: 159 S-RPGERLAQKLLRILSPLGFP--KYK-PIPAETVAKAMVKAALKESSNK 204
>gnl|CDD|200085 TIGR01214, rmlD, dTDP-4-dehydrorhamnose reductase. This enzyme
catalyzes the last of 4 steps in making dTDP-rhamnose, a
precursor of LPS core antigen, O-antigen, etc [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 287
Score = 55.9 bits (135), Expect = 4e-09
Identities = 58/251 (23%), Positives = 87/251 (34%), Gaps = 75/251 (29%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRNDDEIR 82
+ GA+G +G L +L +G ++ R D+ D P + +
Sbjct: 4 ITGANGQLGRELVQQLSPEGRVVVALTRSQL-DLTD----------------PEALERLL 46
Query: 83 KAIKYSNVVINLIGREFATKNFTIADA-----------NVEIPARLARLSKEMGVEKFIH 131
+AI+ + V+N T +T D N P LAR + G + +H
Sbjct: 47 RAIR-PDAVVN-------TAAYTDVDGAESDPEKAFAVNALAPQNLARAAARHGA-RLVH 97
Query: 132 IS-------------ALNADPNPPTYYISGGSQFYRTKYQGEKEVLREFPEATIFRPSDM 178
IS + NP Y ++K GE+ V P A I R S +
Sbjct: 98 ISTDYVFDGEGKRPYREDDATNPLNVY-------GQSKLAGEQAVRAAGPNALIVRTSWL 150
Query: 179 Y--GSGDKFLRYYGHMWRHVFRKLAVYKKGEE------TIKQPVYVGDVAAAIVAACKDP 230
Y G G F+R +LA +GEE I P Y D+A I A +
Sbjct: 151 YGGGGGRNFVR--------TMLRLA--GRGEELRVVDDQIGSPTYAKDLARVIAALLQRL 200
Query: 231 DAAGKIYQAVG 241
A +Y
Sbjct: 201 ARARGVYHLAN 211
>gnl|CDD|216283 pfam01073, 3Beta_HSD, 3-beta hydroxysteroid dehydrogenase/isomerase
family. The enzyme 3 beta-hydroxysteroid
dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD)
catalyzes the oxidation and isomerisation of 5-ene-3
beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid
precursors into the corresponding 4-ene-ketosteroids
necessary for the formation of all classes of steroid
hormones.
Length = 280
Score = 55.0 bits (133), Expect = 1e-08
Identities = 62/259 (23%), Positives = 104/259 (40%), Gaps = 58/259 (22%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVR--DLR----LCGDLGQVLFQPYHP- 75
V G G++G ++ L + G +VR DLR L D ++ Y
Sbjct: 2 VTGGGGFLGRHIVRLLLR---------EGELQEVRVFDLRFSPELLEDFSKLQVITYIEG 52
Query: 76 --RNDDEIRKAIKYSNVVINL--IGREFATKNF-TIADANVEIPARLARLSKEMGVEKFI 130
+ ++R+A++ S+VVI+ I F TI NV+ + + GV +
Sbjct: 53 DVTDKQDLRRALQGSDVVIHTAAIIDVFGKAYRDTIMKVNVKGTQNVLDACVKAGVRVLV 112
Query: 131 HISA-------------LNADPNPPTYYISGGSQFYRTKYQGEKEVLRE----------- 166
+ S+ +N D P Y + + +K EK VL+
Sbjct: 113 YTSSMEVVGPNSYGQPIVNGDETTP-YESTHQDPYPESKALAEKLVLKANGSTLKNGGRL 171
Query: 167 FPEATIFRPSDMYGSGDKFLRYYGHMWRHVFRKLAVYKKGEETIKQ-PVYVGDVAAAIVA 225
+ A RP+ ++G GD FL + + R + LA ++ G++ + VYVG+VA A +
Sbjct: 172 YTCA--LRPAGIFGEGDPFL--FPFLVRLLKNGLAKFRTGDKNVLSDRVYVGNVAWAHIL 227
Query: 226 A-------CKDPDAAGKIY 237
A K AG+ Y
Sbjct: 228 AARALQDPKKASSIAGQFY 246
>gnl|CDD|212494 cd08946, SDR_e, extended (e) SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 200
Score = 53.8 bits (130), Expect = 1e-08
Identities = 43/235 (18%), Positives = 81/235 (34%), Gaps = 60/235 (25%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRNDDEIR 82
V G +G++GS+L +L ++G ++++ D D
Sbjct: 3 VTGGAGFIGSHLVRRLLERGHEVVV------IDRLD------------------------ 32
Query: 83 KAIKYSNVVINLIG----REFATKNFTIADANVEIPARLARLSKEMGVEKFIHIS----- 133
VV++L + NV L +++ GV++F++ S
Sbjct: 33 -------VVVHLAALVGVPASWDNPDEDFETNVVGTLNLLEAARKAGVKRFVYASSASVY 85
Query: 134 ALNADPNPPTYYISGGSQFY-RTKYQGEKEVLREFPEA-----TIFRPSDMYGSGDKFLR 187
Y +K E +LR + E+ I R +++YG G +
Sbjct: 86 GSPEGLPEEEETPPRPLSPYGVSKLAAEH-LLRSYGESYGLPVVILRLANVYGPGQRPRL 144
Query: 188 YYGHMWRHVFRKLAVYKK-----GEETIKQPVYVGDVAAAIVAACKDPDAAGKIY 237
+ R+ K G + ++V DV AI+ A ++P G +Y
Sbjct: 145 D--GVVNDFIRRALEGKPLTVFGGGNQTRDFIHVDDVVRAILHALENPLEGGGVY 197
>gnl|CDD|218026 pfam04321, RmlD_sub_bind, RmlD substrate binding domain.
L-rhamnose is a saccharide required for the virulence of
some bacteria. Its precursor, dTDP-L-rhamnose, is
synthesised by four different enzymes the final one of
which is RmlD. The RmlD substrate binding domain is
responsible for binding a sugar nucleotide.
Length = 284
Score = 54.9 bits (133), Expect = 1e-08
Identities = 38/160 (23%), Positives = 54/160 (33%), Gaps = 49/160 (30%)
Query: 109 ANVEIPARLARLSKEMGVEKFIHISALNADPNPPTYYISGGSQ--------------FY- 153
N P LA G IHIS T Y+ G++ Y
Sbjct: 75 VNALGPGNLAEACAARGA-PLIHIS---------TDYVFDGAKGGPYREDDPTGPLNVYG 124
Query: 154 RTKYQGEKEVLREFPEATIFRPSDMYGSGDK-FLRYYGHMWRHVFRKLAVYKKGEETIK- 211
RTK GE+ VL P I R + +YG F++ +LA + ++
Sbjct: 125 RTKLAGEQAVLAANPRHLILRTAWVYGEYGNNFVK--------TMLRLA---AERDELRV 173
Query: 212 ------QPVYVGDVAAAIVAA----CKDPDAAGKIYQAVG 241
P D+A A++A + P AG Y G
Sbjct: 174 VDDQLGSPTSARDLADALLALIRKRLRGPALAG-TYHLAG 212
>gnl|CDD|187556 cd05245, SDR_a2, atypical (a) SDRs, subgroup 2. This subgroup
contains atypical SDRs, one member is identified as
Escherichia coli protein ybjT, function unknown.
Atypical SDRs are distinct from classical SDRs. Members
of this subgroup have a glycine-rich NAD(P)-binding
motif consensus that generally matches the extended
SDRs, TGXXGXXG, but lacks the characteristic active site
residues of the SDRs. This subgroup has basic residues
(HXXXR) in place of the active site motif YXXXK, these
may have a catalytic role. Atypical SDRs generally lack
the catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 50.0 bits (120), Expect = 4e-07
Identities = 55/230 (23%), Positives = 92/230 (40%), Gaps = 35/230 (15%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQV------LFQPYHPR 76
V GA+GY+G L +L ++G Q+ R L +V L P
Sbjct: 3 VTGATGYVGGRLVPRLLQEGHQVRALVR----SPEKLADRPWSERVTVVRGDLEDP---- 54
Query: 77 NDDEIRKAIKYSNVVINLIGREFATKNFTIADANVEIPARLARLSKEMGVEKFIHISALN 136
+ +R A++ + L+ + +F AD AR ++ GV++ I++ L
Sbjct: 55 --ESLRAALEGIDTAYYLVHSMGSGGDFEEADR--RAARNFARAARAAGVKRIIYLGGLI 110
Query: 137 ADPNPPTYYISGGSQFYRTKYQGEKEVLRE--FPEATIFRPSDMYGSGDKFLRYYGHMWR 194
S R++ + E+LR P T R + + GSG M R
Sbjct: 111 PKGEEL-------SPHLRSRAEVG-EILRAGGVP-VTELRAAVIIGSGSASFE----MVR 157
Query: 195 HVFRKLAVY--KKGEETIKQPVYVGDVAAAIVAACKDPDAAGKIYQAVGP 242
++ +L V + T QP+ + DV +VAA P AG+ ++ GP
Sbjct: 158 YLVERLPVMITPRWVNTPCQPIAIRDVLEYLVAALDRPATAGETFEIGGP 207
>gnl|CDD|187573 cd05263, MupV_like_SDR_e, Pseudomonas fluorescens MupV-like,
extended (e) SDRs. This subgroup of extended SDR family
domains have the characteristic active site tetrad and a
well-conserved NAD(P)-binding motif. This subgroup is
not well characterized, its members are annotated as
having a variety of putative functions. One
characterized member is Pseudomonas fluorescens MupV a
protein involved in the biosynthesis of Mupirocin, a
polyketide-derived antibiotic. Extended SDRs are
distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 293
Score = 48.9 bits (117), Expect = 1e-06
Identities = 54/298 (18%), Positives = 104/298 (34%), Gaps = 48/298 (16%)
Query: 25 GASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLC-------------GDLGQVLFQ 71
G +G++G +L +L + G ++++ R R+ GDL Q
Sbjct: 5 GGTGFLGRHLVKRLLENGFKVLVLVRSESLGEAHERIEEAGLEADRVRVLEGDLTQ---- 60
Query: 72 PYHPR---NDDEIRKAIKYSNVVINLIGR-EFATKNFTIADANVEIPARLARLSKEMGVE 127
P + R+ + VI+ +F N N++ + L+ + ++
Sbjct: 61 ---PNLGLSAAASRELAGKVDHVIHCAASYDFQAPNEDAWRTNIDGTEHVLELAARLDIQ 117
Query: 128 KFIHIS----------ALNADPNPPTYYISGGSQFYRTKYQGEKEVLREFPEA---TIFR 174
+F ++S + P + ++K + E+ ++R T++R
Sbjct: 118 RFHYVSTAYVAGNREGNIRETELNPGQNFKNP--YEQSKAEAEQ-LVRAAATQIPLTVYR 174
Query: 175 PSDMYG--SGDKFLRYYG--HMWRHVFRKLAVYKK--GEETIKQP-VYVGDVAAAIVAAC 227
PS + G + + G + + KL + G + + V V VA AIV
Sbjct: 175 PSIVVGDSKTGRIEKIDGLYELLN-LLAKLGRWLPMPGNKGARLNLVPVDYVADAIVYLS 233
Query: 228 KDPDAAGKIYQAVGPKRYLLSELLDWFHVVMKKGEPDYGYYRYDLRYDPVMPLKLFIN 285
K P+A G+I+ P L E+ D F P + +N
Sbjct: 234 KKPEANGQIFHLTDPTPQTLREIADLFKSAFLSPGLLVLLMNEPNASLPNALRRSLLN 291
>gnl|CDD|187578 cd05269, TMR_SDR_a, triphenylmethane reductase (TMR)-like proteins,
NMRa-like, atypical (a) SDRs. TMR is an atypical
NADP-binding protein of the SDR family. It lacks the
active site residues of the SDRs but has a glycine rich
NAD(P)-binding motif that matches the extended SDRs.
Proteins in this subgroup however, are more similar in
length to the classical SDRs. TMR was identified as a
reducer of triphenylmethane dyes, important
environmental pollutants. This subgroup also includes
Escherichia coli NADPH-dependent quinine oxidoreductase
(QOR2), which catalyzes two-electron reduction of
quinone; but is unlikely to play a major role in
protecting against quinone cytotoxicity. Atypical SDRs
are distinct from classical SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 272
Score = 46.5 bits (111), Expect = 6e-06
Identities = 63/290 (21%), Positives = 101/290 (34%), Gaps = 73/290 (25%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPR-----N 77
V GA+G +G+ + L + + ++ VR+ R +
Sbjct: 3 VTGATGKLGTAVVELLLAKVASVVAL-------VRNPE---KAKAFAADGVEVRQGDYDD 52
Query: 78 DDEIRKAIK-YSNVVI----NLIGREFATKNFTIADANVEIPARLARLSKEMGVEKFIHI 132
+ + +A + +++ +L R KNF I A K+ GV+ +++
Sbjct: 53 PETLERAFEGVDRLLLISPSDLEDRIQQHKNF-IDAA------------KQAGVKHIVYL 99
Query: 133 SALNADPNPPTYYISGGSQFYRTKYQGEKEVLREFPEATIFRPSDMYGSGDKFLRYYGHM 192
SA AD + P R EK + TI RP + D L + +
Sbjct: 100 SASGADEDSP-------FLLARDHGATEKYLEASGIPYTILRPG-WFM--DNLLEFLPSI 149
Query: 193 WRH-VFRKLAVYKKGEETIKQPVYVGDVAAAIVAACKDPDAAGKIYQAVGPKRY------ 245
A G+ + V D+A A AA +P GK+Y GP+
Sbjct: 150 LEEGTIYGPA----GDGKVA-FVDRRDIAEAAAAALTEPGHEGKVYNLTGPEALSYAELA 204
Query: 246 -LLSELLDWFHVVMKKGEPDYGYYRYDLRYDPVMPLKLFINGLFPGYPMG 294
+LSE L G+P +RY PV P + L G P G
Sbjct: 205 AILSEAL---------GKP--------VRYVPVSPDEAARELLAAGLPEG 237
>gnl|CDD|219687 pfam07993, NAD_binding_4, Male sterility protein. This family
represents the C-terminal region of the male sterility
protein in a number of arabidopsis and drosophila. A
sequence-related jojoba acyl CoA reductase is also
included.
Length = 245
Score = 41.0 bits (97), Expect = 3e-04
Identities = 40/208 (19%), Positives = 69/208 (33%), Gaps = 74/208 (35%)
Query: 25 GASGYMGSYLCNKL-----------------GKQGSQIIIP---YRGNFYDVRDLR---- 60
GA+G++G L KL G+ + + G F ++ L
Sbjct: 3 GATGFLGKVLLEKLLRSTPEVKIYCLVRAKDGESALERLRQELLKYGLFDRLKALERIIP 62
Query: 61 LCGDLGQVLFQPYHPR---NDDEIRKAIKYSNVVINLIGREFATKNF-----TIADANVE 112
+ GDL + P +D++ ++ + +V+I+ AT NF + NV
Sbjct: 63 VAGDLSE-------PNLGLSDEDFQELAEEVDVIIHNA----ATVNFVEPYSDLRATNVL 111
Query: 113 IPARLARLSKEMGVEKFIHIS----------------------ALNADPNPPTYYISGGS 150
+ RL+K+M F H+S P Y
Sbjct: 112 GTREVLRLAKQMKKLPFHHVSTAYVNGERGGLLEEKPYKLDEDEPALLGGLPNGYT---- 167
Query: 151 QFYRTKYQGEKEVLREFPE--ATIFRPS 176
++K+ E+ V I+RPS
Sbjct: 168 ---QSKWLAEQLVREAAGGLPVVIYRPS 192
>gnl|CDD|224015 COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase
[General function prediction only].
Length = 297
Score = 40.3 bits (95), Expect = 7e-04
Identities = 34/159 (21%), Positives = 56/159 (35%), Gaps = 36/159 (22%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRNDDEIR 82
+ G +G +G L +L K G Q+ I R R + +L + + +
Sbjct: 3 ITGGTGLIGRALTARLRKGGHQVTILTR------RPPKASQNL------HPNVTLWEGLA 50
Query: 83 KAIKYS-NVVINLIGREFATKNFT------IADANVEIPARLARLSKEMGVEKFIHISAL 135
A+ + VINL G A + +T I + + +L L I+A
Sbjct: 51 DALTLGIDAVINLAGEPIAERRWTEKQKEEIRQSRINTTEKLVEL-----------IAAS 99
Query: 136 NADPNPPTYYISGGS-QFYRTKYQGEKEVLREFPEATIF 173
P IS + +Y G++ V E P F
Sbjct: 100 ET---KPKVLISASAVGYYGH--SGDRVVTEESPPGDDF 133
>gnl|CDD|187552 cd05241, 3b-HSD-like_SDR_e, 3beta-hydroxysteroid dehydrogenases
(3b-HSD)-like, extended (e) SDRs. Extended SDR family
domains belonging to this subgroup have the
characteristic active site tetrad and a fairly
well-conserved NAD(P)-binding motif. 3b-HSD catalyzes
the NAD-dependent conversion of various steroids, such
as pregnenolone to progesterone, or androstenediol to
testosterone. This subgroup includes an unusual
bifunctional 3b-HSD/C-4 decarboxylase from Arabidopsis
thaliana, and Saccharomyces cerevisiae ERG26, a
3b-HSD/C-4 decarboxylase, involved in the synthesis of
ergosterol, the major sterol of yeast. It also includes
human 3 beta-HSD/HSD3B1 and C(27) 3beta-HSD/
[3beta-hydroxy-delta(5)-C(27)-steroid oxidoreductase;
HSD3B7]. C(27) 3beta-HSD/HSD3B7 is a membrane-bound
enzyme of the endoplasmic reticulum, that catalyzes the
isomerization and oxidation of 7alpha-hydroxylated
sterol intermediates, an early step in bile acid
biosynthesis. Mutations in the human NSDHL (NAD(P)H
steroid dehydrogenase-like protein) cause CHILD syndrome
(congenital hemidysplasia with ichthyosiform nevus and
limb defects), an X-linked dominant, male-lethal trait.
Mutations in the human gene encoding C(27) 3beta-HSD
underlie a rare autosomal recessive form of neonatal
cholestasis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase have
a GGXGXXG NAD(P)-binding motif and an altered active
site motif (YXXXN). Fungal type ketoacyl reductases have
a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 331
Score = 38.6 bits (90), Expect = 0.003
Identities = 52/250 (20%), Positives = 94/250 (37%), Gaps = 55/250 (22%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHP------- 75
V G SG+ G L +L ++G + +D+ + L HP
Sbjct: 4 VTGGSGFFGERLVKQLLERGGTYVR-----SFDIAPPG------EALSAWQHPNIEFLKG 52
Query: 76 --RNDDEIRKAIKYSNVVINL--IGREFATKNFTIADANVEIPARLARLSKEMGVEKFIH 131
+ +++ +A+ ++ V + I ++ + NV + + GV+KF++
Sbjct: 53 DITDRNDVEQALSGADCVFHTAAIVPLAGPRDL-YWEVNVGGTQNVLDACQRCGVQKFVY 111
Query: 132 ISAL----------NAD---PNPPTYYISGGSQFY-RTKYQGEKEVL----REFPEATIF 173
S+ N D P PP S Y TK E VL R+
Sbjct: 112 TSSSSVIFGGQNIHNGDETLPYPPLD-----SDMYAETKAIAEIIVLEANGRDDLLTCAL 166
Query: 174 RPSDMYGSGDKFLRYYGHMWRHVFRKLA--VYKKGEETIKQPVYVGDVAAAIVAAC---- 227
RP+ ++G GD+ L ++ + L V+ +G + YV ++A A + A
Sbjct: 167 RPAGIFGPGDQGL--VPILFEWAEKGLVKFVFGRGNNLV-DFTYVHNLAHAHILAAAALV 223
Query: 228 KDPDAAGKIY 237
K +G+ Y
Sbjct: 224 KGKTISGQTY 233
>gnl|CDD|187546 cd05235, SDR_e1, extended (e) SDRs, subgroup 1. This family
consists of an SDR module of multidomain proteins
identified as putative polyketide sythases fatty acid
synthases (FAS), and nonribosomal peptide synthases,
among others. However, unlike the usual ketoreductase
modules of FAS and polyketide synthase, these domains
are related to the extended SDRs, and have canonical
NAD(P)-binding motifs and an active site tetrad.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 290
Score = 37.6 bits (88), Expect = 0.004
Identities = 58/304 (19%), Positives = 98/304 (32%), Gaps = 98/304 (32%)
Query: 22 TVF--GASGYMGSYLCNKL--------------GKQGSQI-------IIPYRGNFYDVRD 58
TV GA+G++G+YL +L K + Y N +D +
Sbjct: 1 TVLLTGATGFLGAYLLRELLKRKNVSKIYCLVRAKDEEAALERLIDNLKEYGLNLWDELE 60
Query: 59 LR----LCGDLGQVLF----QPYHPRNDDEIRKAIKYSNVVINLIGREFATKNF-----T 105
L + GDL + Y E+ + + +V+I+ G A N+
Sbjct: 61 LSRIKVVVGDLSKPNLGLSDDDY-----QELAEEV---DVIIH-NG---ANVNWVYPYEE 108
Query: 106 IADANVEIPARLARLSKEMGVEKFIHISALNA-------------DPNPPTYYISGGSQF 152
+ ANV L +L+ ++ +S L+ + + +
Sbjct: 109 LKPANVLGTKELLKLAATGKLKPLHFVSTLSVFSAEEYNALDDEESDDMLESQNGLPNGY 168
Query: 153 YRTKYQGEKEVLREF----PEATIFRPSDMYG--------SGDKFLR---------YYGH 191
++K+ EK +LRE I RP +++G + D F R Y
Sbjct: 169 IQSKWVAEK-LLREAANRGLPVAIIRPGNIFGDSETGIGNTDDFFWRLLKGCLQLGIYPI 227
Query: 192 MWRHVFRKLAVYKKGEETIKQPVYVGDVAAAIVAACKDPDAAGKIYQAVGPKRYLLSELL 251
+ V VA AIV + IY + P L++LL
Sbjct: 228 SGAPLDL---------------SPVDWVARAIVKLALNESNEFSIYHLLNPPLISLNDLL 272
Query: 252 DWFH 255
D
Sbjct: 273 DALE 276
>gnl|CDD|233570 TIGR01777, yfcH, TIGR01777 family protein. This model represents a
clade of proteins of unknown function including the E.
coli yfcH protein [Hypothetical proteins, Conserved].
Length = 291
Score = 37.6 bits (88), Expect = 0.006
Identities = 30/155 (19%), Positives = 53/155 (34%), Gaps = 34/155 (21%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRNDDEIR 82
+ G +G++G L +L K+G ++ I R + ++P+ + D +
Sbjct: 3 ITGGTGFIGRALTQRLTKRGHEVTIL-------TRSPPPGANTKWEGYKPWAGEDADSLE 55
Query: 83 KAIKYSNVVINLIGREFATKNFT------IADANVEIPARLARLSKEMGVEKFIHISALN 136
A + VINL G A K +T I D+ ++ L
Sbjct: 56 GA----DAVINLAGEPIADKRWTEERKQEIRDSRIDTTRLLVEAIAAA------------ 99
Query: 137 ADPNPPTYYISG-GSQFYRTKYQGEKEVLREFPEA 170
P +IS +Y ++E E A
Sbjct: 100 --EQKPKVFISASAVGYYGP--SEDREYTEEDSPA 130
>gnl|CDD|191263 pfam05368, NmrA, NmrA-like family. NmrA is a negative
transcriptional regulator involved in the
post-translational modification of the transcription
factor AreA. NmrA is part of a system controlling
nitrogen metabolite repression in fungi. This family
only contains a few sequences as iteration results in
significant matches to other Rossmann fold families.
Length = 232
Score = 37.2 bits (87), Expect = 0.006
Identities = 47/254 (18%), Positives = 75/254 (29%), Gaps = 81/254 (31%)
Query: 22 TVFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLR--------------LCGDLGQ 67
VFGA+GY G + K G + VRD + + GDL
Sbjct: 2 LVFGATGYQGGSVVRASLKAGHPV-------RALVRDPKSELAKSLKAAGVELVEGDLD- 53
Query: 68 VLFQPYHPRNDDEIRKAIKYSNVVINLIGREFATKNFTIADANVEIPARLARLSKEMGVE 127
+ + + +A+K +VV F+ F +E +LA +KE GV+
Sbjct: 54 ---------DHESLVEALKGVDVV-------FSVTGFW-LSKEIEDGKKLADAAKEAGVK 96
Query: 128 KFIHISALNADPNPPTYYISGGSQ----FYRTKYQGEKEVLRE-FPEATIFRP------- 175
FI N S G + + +K + E+ + P T
Sbjct: 97 HFIPSEFGNDVD------RSNGVEPAVPHFDSKAEVERYIRALGIP-YTFVYAGFFMGNF 149
Query: 176 -------SDMYGSGDKFLRYYGHMWRHVFRKLAVYKKGEETIKQPVYVGDVAAAIVAACK 228
D+ DK + G D+ ++
Sbjct: 150 LSNLAPPGDLAPPRDKV---------------TLLGPGNPKAVPLDDEEDIGTYVIKILD 194
Query: 229 DPDAA-GKIYQAVG 241
DP GK + G
Sbjct: 195 DPRKLKGKYIRPPG 208
>gnl|CDD|187576 cd05266, SDR_a4, atypical (a) SDRs, subgroup 4. Atypical SDRs in
this subgroup are poorly defined, one member is
identified as a putative NAD-dependent
epimerase/dehydratase. Atypical SDRs are distinct from
classical SDRs. Members of this subgroup have a
glycine-rich NAD(P)-binding motif that is related to,
but is different from, the archetypical SDRs, GXGXXG.
This subgroup also lacks most of the characteristic
active site residues of the SDRs; however, the upstream
Ser is present at the usual place, and some potential
catalytic residues are present in place of the usual
YXXXK active site motif. Atypical SDRs generally lack
the catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 251
Score = 35.0 bits (81), Expect = 0.033
Identities = 50/255 (19%), Positives = 84/255 (32%), Gaps = 63/255 (24%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIII----PYRGNFYDVRDLRLCGDLGQVLFQPYHPRND 78
+ G GY+G L +L QG Q+ P + + L L QP +
Sbjct: 3 ILGC-GYLGQRLARQLLAQGWQVTGTTRSPEKLAADRPAGVT---PLAADLTQPGLLADV 58
Query: 79 DEIRKAIKYSNVVINLIGREFATKNFTIADANVEIPARLAR-LSKEMGVEKFIHISA--- 134
D ++VI+L + L L++ V++ I++S+
Sbjct: 59 D---------HLVISL-----PPPAGSYRGGYDPGLRALLDALAQLPAVQRVIYLSSTGV 104
Query: 135 ---------LNADPNPPTYYISGGSQFYRTKYQGEKEVLREF-PEATIFRPSDMYGSGDK 184
P P+ ++ R + E+ +L TI R + +YG G
Sbjct: 105 YGDQQGEWVDETSPPNPS------TESGRALLEAEQALLALGSKPTTILRLAGIYGPG-- 156
Query: 185 FLRYYGHMWRHVFRKLAVYKKGEETIKQP------VYVGDVAAAIVAACKDPDAAGKIYQ 238
RH R+LA +G ++V D+ A+ A + P A G +Y
Sbjct: 157 ---------RHPLRRLA---QGTGRPPAGNAPTNRIHVDDLVGALAFALQRP-APGPVYN 203
Query: 239 AVGPKRYLLSELLDW 253
V E
Sbjct: 204 VVDDLPVTRGEFYQA 218
>gnl|CDD|187566 cd05256, UDP_AE_SDR_e, UDP-N-acetylglucosamine 4-epimerase,
extended (e) SDRs. This subgroup contains
UDP-N-acetylglucosamine 4-epimerase of Pseudomonas
aeruginosa, WbpP, an extended SDR, that catalyzes the
NAD+ dependent conversion of UDP-GlcNAc and UDPGalNA to
UDP-Glc and UDP-Gal. This subgroup has the
characteristic active site tetrad and NAD-binding motif
of the extended SDRs. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 304
Score = 34.5 bits (80), Expect = 0.049
Identities = 66/276 (23%), Positives = 113/276 (40%), Gaps = 47/276 (17%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRNDDEIR 82
V G +G++GS+L +L ++G ++I+ N + L V F R+D+ +
Sbjct: 4 VTGGAGFIGSHLVERLLERGHEVIV--LDNLSTGKKENLPEVKPNVKFIEGDIRDDELVE 61
Query: 83 KAIKYSNVVINLIGREFATKNFTIAD------ANVEIPARLARLSKEMGVEKFIHISALN 136
A + + V + A+ +I D NV L +++ GV++F++ S+ +
Sbjct: 62 FAFEGVDYVFHQAA--QASVPRSIEDPIKDHEVNVLGTLNLLEAARKAGVKRFVYASSSS 119
Query: 137 ADPNPPTY------YISGGSQFYRTKYQGEKEVLREFPEATIFRPSDMYGSGDKFLRY-- 188
+PP + S + +KY GE + F +YG LRY
Sbjct: 120 VYGDPPYLPKDEDHPPNPLSPYAVSKYAGE-LYCQVFAR--------LYGLPTVSLRYFN 170
Query: 189 -YG------HMWRHVF-----RKLA-----VYKKGEETIKQPVYVGDVAAAIVAACKDPD 231
YG + V R L +Y GE+T + YV DV A + A
Sbjct: 171 VYGPRQDPNGGYAAVIPIFIERALKGEPPTIYGDGEQT-RDFTYVEDVVEANLLAATA-G 228
Query: 232 AAGKIYQAVGPKRYLLSELLDWF-HVVMKKGEPDYG 266
A G++Y KR ++EL + ++ K+ EP Y
Sbjct: 229 AGGEVYNIGTGKRTSVNELAELIREILGKELEPVYA 264
>gnl|CDD|236216 PRK08277, PRK08277, D-mannonate oxidoreductase; Provisional.
Length = 278
Score = 33.3 bits (77), Expect = 0.12
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 15 SFNGVVATVFGASGYMGSYLCNKLGKQGSQIII 47
S G VA + G G +G + +L + G+++ I
Sbjct: 7 SLKGKVAVITGGGGVLGGAMAKELARAGAKVAI 39
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 32.7 bits (75), Expect = 0.14
Identities = 25/155 (16%), Positives = 53/155 (34%), Gaps = 29/155 (18%)
Query: 77 NDDEIRKAIKYSNVVINLIG-REFATKNFTIADANVEIPARLARLSKEMGVEKFIHISAL 135
+ ++ +A+ + V++ G R + L + GV + + +SA
Sbjct: 49 DLADLAEALAGVDAVVDAFGARPDDSDGV----------KHLLDAAARAGVRRIVVVSAA 98
Query: 136 NADPN-PPTYYISGGSQF---YRTKYQGEKEVLREFPEATIFRPSDMYGSGDKFLRYYGH 191
+ P T+ + F R K E+ + + TI RP ++
Sbjct: 99 GLYRDEPGTFRLDDAPLFPPYARAKAAAEELLRASGLDWTIVRPGALFDEEG-------- 150
Query: 192 MWRHVFRKLAVYKKGEETIKQPVYVGDVAAAIVAA 226
+ +G+ + + DVAAA++
Sbjct: 151 ------ETYEIGTEGDPAGESSISRADVAAALLDE 179
>gnl|CDD|235500 PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 248
Score = 32.1 bits (74), Expect = 0.24
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 15 SFNGVVATVFGASGYMGSYLCNKLGKQGSQIIIPYRGN 52
S G VA V GAS +G + +L QG+ ++I Y +
Sbjct: 2 SLEGKVALVTGASRGIGRAIAERLAAQGANVVINYASS 39
>gnl|CDD|181585 PRK08936, PRK08936, glucose-1-dehydrogenase; Provisional.
Length = 261
Score = 32.0 bits (73), Expect = 0.26
Identities = 32/136 (23%), Positives = 55/136 (40%), Gaps = 35/136 (25%)
Query: 14 SSFNGVVATVFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPY 73
S G V + G S +G + + GK+ ++++I YR + + D+
Sbjct: 3 SDLEGKVVVITGGSTGLGRAMAVRFGKEKAKVVINYRSDEEEANDVA------------- 49
Query: 74 HPRNDDEIRKA-----IKYSNV-----VINLIG---REFATKNFTIADANVEIPARLARL 120
+EI+KA +V V+NLI +EF T + I +A +E
Sbjct: 50 -----EEIKKAGGEAIAVKGDVTVESDVVNLIQTAVKEFGTLDVMINNAGIENAVP---- 100
Query: 121 SKEMGVEKFIHISALN 136
S EM +E + + N
Sbjct: 101 SHEMSLEDWNKVINTN 116
>gnl|CDD|187574 cd05264, UDP_G4E_5_SDR_e, UDP-glucose 4-epimerase (G4E), subgroup
5, extended (e) SDRs. This subgroup partially conserves
the characteristic active site tetrad and NAD-binding
motif of the extended SDRs, and has been identified as
possible UDP-glucose 4-epimerase (aka UDP-galactose
4-epimerase), a homodimeric member of the extended SDR
family. UDP-glucose 4-epimerase catalyzes the
NAD-dependent conversion of UDP-galactose to
UDP-glucose, the final step in Leloir galactose
synthesis. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 300
Score = 32.3 bits (74), Expect = 0.27
Identities = 46/235 (19%), Positives = 87/235 (37%), Gaps = 45/235 (19%)
Query: 21 ATVFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRNDDE 80
+ G +G++GS+L + L ++G Q+ + +D LG V + N +
Sbjct: 2 VLIVGGNGFIGSHLVDALLEEGPQVRV------FDRSIPPYELPLGGVDYIKGDYENRAD 55
Query: 81 IRKAIKYSNVVINLIGREF-ATKNFTIA---DANVEIPARLARLSKEMGVEKFIHIS--- 133
+ A+ + VI+L AT N NV +L G+ K I S
Sbjct: 56 LESALVGIDTVIHLASTTNPATSNKNPILDIQTNVAPTVQLLEACAAAGIGKIIFASSGG 115
Query: 134 -----------ALNADPNPPTYY------ISGGSQFYRTKYQGEKEVLREFPEATIFRPS 176
+ + P + Y I + Y+ Y + T+ R S
Sbjct: 116 TVYGVPEQLPISESDPTLPISSYGISKLAIEKYLRLYQYLYGL---------DYTVLRIS 166
Query: 177 DMYGSGDKFLRYYG----HMWRHVF-RKLAVYKKGEETIKQPVYVGDVAAAIVAA 226
+ YG G + G + + + + ++ G E+I+ +Y+ D+ A++A
Sbjct: 167 NPYGPGQRPDGKQGVIPIALNKILRGEPIEIWGDG-ESIRDYIYIDDLVEALMAL 220
>gnl|CDD|188169 TIGR01829, AcAcCoA_reduct, acetoacetyl-CoA reductase. This model
represent acetoacetyl-CoA reductase, a member of the
family short-chain-alcohol dehydrogenases. Note that,
despite the precision implied by the enzyme name, the
reaction of EC 1.1.1.36 is defined more generally as
(R)-3-hydroxyacyl-CoA + NADP+ = 3-oxoacyl-CoA + NADPH.
Members of this family may act in the biosynthesis of
poly-beta-hydroxybutyrate (e.g. Rhizobium meliloti) and
related poly-beta-hydroxyalkanoates. Note that the
member of this family from Azospirillum brasilense,
designated NodG, appears to lack acetoacetyl-CoA
reductase activity and to act instead in the production
of nodulation factor. This family is downgraded to
subfamily for this NodG. Other proteins designated
NodG, as from Rhizobium, belong to related but distinct
protein families.
Length = 242
Score = 32.0 bits (73), Expect = 0.28
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 20 VATVFGASGYMGSYLCNKLGKQGSQIIIPYRGNF 53
+A V G G +G+ +C +L K G ++ N
Sbjct: 2 IALVTGGMGGIGTAICQRLAKDGYRVAANCGPNE 35
>gnl|CDD|187561 cd05251, NmrA_like_SDR_a, NmrA (a transcriptional regulator) and
HSCARG (an NADPH sensor) like proteins, atypical (a)
SDRs. NmrA and HSCARG like proteins. NmrA is a negative
transcriptional regulator of various fungi, involved in
the post-translational modulation of the GATA-type
transcription factor AreA. NmrA lacks the canonical
GXXGXXG NAD-binding motif and has altered residues at
the catalytic triad, including a Met instead of the
critical Tyr residue. NmrA may bind nucleotides but
appears to lack any dehydrogenase activity. HSCARG has
been identified as a putative NADP-sensing molecule, and
redistributes and restructures in response to NADPH/NADP
ratios. Like NmrA, it lacks most of the active site
residues of the SDR family, but has an NAD(P)-binding
motif similar to the extended SDR family, GXXGXXG. SDRs
are a functionally diverse family of oxidoreductases
that have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Atypical SDRs
are distinct from classical SDRs. Classical SDRs have an
TGXXX[AG]XG cofactor binding motif and a YXXXK active
site motif, with the Tyr residue of the active site
motif serving as a critical catalytic residue (Tyr-151,
human 15-hydroxyprostaglandin dehydrogenase numbering).
In addition to the Tyr and Lys, there is often an
upstream Ser and/or an Asn, contributing to the active
site; while substrate binding is in the C-terminal
region, which determines specificity. The standard
reaction mechanism is a 4-pro-S hydride transfer and
proton relay involving the conserved Tyr and Lys, a
water molecule stabilized by Asn, and nicotinamide. In
addition to the Rossmann fold core region typical of all
SDRs, extended SDRs have a less conserved C-terminal
extension of approximately 100 amino acids, and
typically have a TGXXGXXG cofactor binding motif.
Complex (multidomain) SDRs such as ketoreductase domains
of fatty acid synthase have a GGXGXXG NAD(P)-binding
motif and an altered active site motif (YXXXN). Fungal
type ketoacyl reductases have a TGXXXGX(1-2)G
NAD(P)-binding motif.
Length = 242
Score = 31.9 bits (73), Expect = 0.32
Identities = 47/265 (17%), Positives = 81/265 (30%), Gaps = 80/265 (30%)
Query: 22 TVFGASGYMGSYLCN-----------------------KLGKQGSQIIIPYRGNFYDVRD 58
VFGA+G G + L G +++ +G+ D
Sbjct: 2 LVFGATGKQGGSVVRALLKDPGFKVRALTRDPSSPAAKALAAPGVEVV---QGDLDDPES 58
Query: 59 LR--LCGDLGQVLFQPYHP-RNDDEIRKAIKYSNVVINLIGREFATKNFTIADANVEIPA 115
L L G G L + +DEI + + DA
Sbjct: 59 LEAALKGVYGVFLVTDFWEAGGEDEIAQGKN-------------------VVDA------ 93
Query: 116 RLARLSKEMGVEKFIHISALNADPNPPTYYISGGSQFYRTKYQGEKEVLREFPEATIFRP 175
+K GV+ F+ S + + ++ + +K + E+ + ATI RP
Sbjct: 94 -----AKRAGVQHFVFSSVPDVEK------LTLAVPHFDSKAEVEEYIRASGLPATILRP 142
Query: 176 SDMYGSGDKFLRYYGHMWRHVFRK-----LAVYKKGEETIKQPVYVGDVAAAIVAACKDP 230
+ + FL + L + + + + V D+ A+ A KDP
Sbjct: 143 AFFM---ENFLT----PPAPQKMEDGTLTLVLPLDPDTKLPM-IDVADIGPAVAAIFKDP 194
Query: 231 DA-AGKIYQAVGPKRYLLSELLDWF 254
GK + G E+ F
Sbjct: 195 AKFNGKTIELAGD-ELTPEEIAAAF 218
>gnl|CDD|187540 cd05229, SDR_a3, atypical (a) SDRs, subgroup 3. These atypical SDR
family members of unknown function have a glycine-rich
NAD(P)-binding motif consensus that is very similar to
the extended SDRs, GXXGXXG. Generally, this group has
poor conservation of the active site tetrad, However,
individual sequences do contain matches to the YXXXK
active site motif, and generally Tyr or Asn in place of
the upstream Ser found in most SDRs. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 302
Score = 31.5 bits (72), Expect = 0.44
Identities = 44/235 (18%), Positives = 84/235 (35%), Gaps = 38/235 (16%)
Query: 21 ATVFGASGYMGSYLCNKLGKQGSQIIIPYR---GNFYDVRDLRLCGDLGQVLFQPYHPRN 77
A V GASG +G + +L ++G + + R + + D
Sbjct: 2 AHVLGASGPIGREVARELRRRGWDVRLVSRSGSKLAWLPGVEIVAADAMDA--------- 52
Query: 78 DDEIRKAIKYSNVVINLIG---REFATKNFTIADANVEIPARLARLSKEMGVEKFIHISA 134
+ A + ++V+ + + + + V + E K +
Sbjct: 53 -SSVIAAARGADVIYHCANPAYTRWEELFPPLMENVVA--------AAEANGAKLVLPGN 103
Query: 135 LNADPNPPTYYISGGSQFYRTKYQG------EKEVLREFP----EATIFRPSDMYGSG-- 182
+ I+ + F T +G E+ +L A I R D YG G
Sbjct: 104 VYMYGPQAGSPITEDTPFQPTTRKGRIRAEMEERLLAAHAKGDIRALIVRAPDFYGPGAI 163
Query: 183 DKFLRYYGHMWRHVFRKLAVYKKGEETIKQPVYVGDVAAAIVAACKDPDAAGKIY 237
+ +L ++ + K AV+ +T + Y+ DVA A+V ++PDA G+ +
Sbjct: 164 NSWLG--AALFAILQGKTAVFPGNLDTPHEWTYLPDVARALVTLAEEPDAFGEAW 216
>gnl|CDD|213592 TIGR01179, galE, UDP-glucose-4-epimerase GalE. Alternate name:
UDPgalactose 4-epimerase This enzyme interconverts
UDP-glucose and UDP-galactose. A set of related
proteins, some of which are tentatively identified as
UDP-glucose-4-epimerase in Thermotoga maritima,
Bacillus halodurans, and several archaea, but deeply
branched from this set and lacking experimental
evidence, are excluded from This model and described by
a separate model [Energy metabolism, Sugars].
Length = 328
Score = 31.5 bits (72), Expect = 0.48
Identities = 9/25 (36%), Positives = 17/25 (68%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIII 47
V G +GY+GS+ +L + G +++I
Sbjct: 4 VTGGAGYIGSHTVRQLLESGHEVVI 28
>gnl|CDD|215029 PLN00016, PLN00016, RNA-binding protein; Provisional.
Length = 378
Score = 31.6 bits (72), Expect = 0.54
Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 12/79 (15%)
Query: 171 TIFRPSDMYGSGDKFLRYYGHMWRHVF------RKLAVYKKGEETIKQPVYVGDVAAAIV 224
T FRP +YG G+ F R + + G + + Q +V D+A+
Sbjct: 204 TSFRPQYIYGPGN-----NKDCEEWFFDRLVRGRPVPIPGSGIQ-LTQLGHVKDLASMFA 257
Query: 225 AACKDPDAAGKIYQAVGPK 243
+P AAG+I+ V +
Sbjct: 258 LVVGNPKAAGQIFNIVSDR 276
>gnl|CDD|188140 TIGR01422, phosphonatase, phosphonoacetaldehyde hydrolase. This
enzyme catalyzes the cleavage of the carbon phosphorous
bond of a phosphonate. The mechanism depends on the
substrate having a carbonyl one carbon away from the
cleavage position. This enzyme is a member of the
Haloacid Dehalogenase (HAD) superfamily of
aspartate-nucleophile hydrolases (pfam00702), and
contains a modified version of the conserved catalytic
motifs of that superfamily: the first motif is usually
DxDx(T/V), here it is DxAxT, and in the third motif the
normal conserved lysine is instead an arginine.
Additionally, the enzyme contains a unique conserved
catalytic lysine (B. cereus pos. 53) which is involved
in the binding and activation of the substrate through
the formation of a Schiff base. The substrate of this
enzyme is the product of 2-aminoethylphosphonate (AEP)
transaminase, phosphonoacetaldehyde. This degradation
pathway for AEP may be related to its toxic properties
which are utilized by microorganisms as a chemical
warfare agent [Central intermediary metabolism, Other].
Length = 253
Score = 30.4 bits (69), Expect = 0.99
Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 99 FA-TKNFTIADANVEIPARLARLSKEMGVEKFIHISALNADP 139
FA T F A A + L K MG+ K+ HI AL P
Sbjct: 19 FAPTGAFVEAFAEFGVQITLEEARKPMGLGKWDHIRALLKMP 60
>gnl|CDD|178047 PLN02427, PLN02427, UDP-apiose/xylose synthase.
Length = 386
Score = 30.2 bits (68), Expect = 1.5
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 25 GASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDL---GQVLFQPYHPRNDDEI 81
GA G++GS+LC KL + ++ ++ L + G++ F + ++D +
Sbjct: 21 GAGGFIGSHLCEKLMTETPHKVLALDVYNDKIKHLLEPDTVPWSGRIQFHRINIKHDSRL 80
Query: 82 RKAIKYSNVVINL 94
IK +++ INL
Sbjct: 81 EGLIKMADLTINL 93
>gnl|CDD|219293 pfam07093, SGT1, SGT1 protein. This family consists of several
eukaryotic SGT1 proteins. Human SGT1 or hSGT1 is known
to suppress GCR2 and is highly expressed in the muscle
and heart. The function of this family is unknown
although it has been speculated that SGT1 may be
functionally analogous to the Gcr2p protein of
Saccharomyces cerevisiae which is known to be a
regulatory factor of glycolytic gene expression.
Length = 557
Score = 30.1 bits (68), Expect = 1.6
Identities = 23/84 (27%), Positives = 32/84 (38%), Gaps = 6/84 (7%)
Query: 40 KQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRNDDEIRKAIKYSNVVINLIGREF 99
G IIP F R L L L + P EI+ AIK L G
Sbjct: 125 HNGELHIIPPSITFLQDRPLTLPEALEILSSSPSKLLASPEIQSAIKK-----RLKGYPE 179
Query: 100 ATKNFTIADANVEIPARLARLSKE 123
K + A V +P ++A++ K+
Sbjct: 180 KIKE-NLHRALVTLPRKVAKVLKQ 202
>gnl|CDD|187553 cd05242, SDR_a8, atypical (a) SDRs, subgroup 8. This subgroup
contains atypical SDRs of unknown function. Proteins in
this subgroup have a glycine-rich NAD(P)-binding motif
consensus that resembles that of the extended SDRs,
(GXXGXXG or GGXGXXG), but lacks the characteristic
active site residues of the SDRs. A Cys often replaces
the usual Lys of the YXXXK active site motif, while the
upstream Ser is generally present and Arg replaces the
usual Asn. Atypical SDRs generally lack the catalytic
residues characteristic of the SDRs, and their
glycine-rich NAD(P)-binding motif is often different
from the forms normally seen in classical or extended
SDRs. Atypical SDRs include biliverdin IX beta reductase
(BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 296
Score = 29.9 bits (68), Expect = 1.7
Identities = 35/184 (19%), Positives = 57/184 (30%), Gaps = 46/184 (25%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRNDDEIR 82
+ G +G++G L +L G ++++ R R + G + +
Sbjct: 4 ITGGTGFIGRALTRRLTAAGHEVVVLSR------RPGKAEGLAEVITWDG-----LSLGP 52
Query: 83 KAIKYSNVVINLIGREFATKNFT------IADANVEIPARLARLSKEMGVEKFIHISALN 136
+ ++ VINL G A + +T I + +E L A+
Sbjct: 53 WELPGADAVINLAGEPIACRRWTEANKKEILSSRIESTRVLVE--------------AIA 98
Query: 137 ADPNPPTYYISG-GSQFYRTKYQGEKEVLREFPEATIFRPSDMYGSGDKFLRYYGHMWRH 195
P PP IS +Y EVL E SG FL W
Sbjct: 99 NAPAPPKVLISASAVGYYGHS---GDEVLTEN-----------SPSGKDFLAEVCKAWEK 144
Query: 196 VFRK 199
+
Sbjct: 145 AAQP 148
>gnl|CDD|187555 cd05244, BVR-B_like_SDR_a, biliverdin IX beta reductase (BVR-B, aka
flavin reductase)-like proteins; atypical (a) SDRs.
Human BVR-B catalyzes pyridine nucleotide-dependent
production of bilirubin-IX beta during fetal
development; in the adult BVR-B has flavin and ferric
reductase activities. Human BVR-B catalyzes the
reduction of FMN, FAD, and riboflavin. Recognition of
flavin occurs mostly by hydrophobic interactions,
accounting for the broad substrate specificity. Atypical
SDRs are distinct from classical SDRs. BVR-B does not
share the key catalytic triad, or conserved tyrosine
typical of SDRs. The glycine-rich NADP-binding motif of
BVR-B is GXXGXXG, which is similar but not identical to
the pattern seen in extended SDRs. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Atypical SDRs include
biliverdin IX beta reductase (BVR-B,aka flavin
reductase), NMRa (a negative transcriptional regulator
of various fungi), progesterone 5-beta-reductase like
proteins, phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 207
Score = 29.5 bits (67), Expect = 1.7
Identities = 37/226 (16%), Positives = 79/226 (34%), Gaps = 37/226 (16%)
Query: 22 TVFGASGYMGSYLCNKLGKQGSQIIIPYRG---NFYDVRDLRLC-GDLGQVLFQPYHPRN 77
+ GA+G GS + + +G ++ R + L++ GD+ +
Sbjct: 3 AIIGATGRTGSAIVREALARGHEVTALVRDPAKLPAEHEKLKVVQGDV----------LD 52
Query: 78 DDEIRKAIKYSNVVINLIGREFATKNFTIADANVEIPARLARLSKEMGVEKFIHISALNA 137
+++++A++ + VI+ +G + + + E + K GV++ I + +
Sbjct: 53 LEDVKEALEGQDAVISALG---TRNDLSPTTLHSEGTRNIVSAMKAAGVKRLIVVGGAGS 109
Query: 138 DPNPPT----YYISGGSQFYRTKYQGEKEVLREFPEA----TIFRPSDMYGSGDKFLRYY 189
+ P R + +L+ E+ T RP ++ G Y
Sbjct: 110 LDDRPKVTLVLDTLLFPPALRRVAEDHARMLKVLRESGLDWTAVRPPALFDGGATGGYYR 169
Query: 190 GHMWRHVFRKLAVYKKGEETIKQPVYVGDVAAAIVAACKDPDAAGK 235
L V KG I D+A ++ + P+ K
Sbjct: 170 VE--------LLVDAKGGSRIS----RADLAIFMLDELETPEHVRK 203
>gnl|CDD|182639 PRK10675, PRK10675, UDP-galactose-4-epimerase; Provisional.
Length = 338
Score = 29.8 bits (67), Expect = 2.0
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIII 47
V G SGY+GS+ C +L + G ++I
Sbjct: 5 VTGGSGYIGSHTCVQLLQNGHDVVI 29
>gnl|CDD|181466 PRK08558, PRK08558, adenine phosphoribosyltransferase; Provisional.
Length = 238
Score = 29.6 bits (67), Expect = 2.0
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 118 ARLSKEMGVEKFIHISALNADPNPPTYYI 146
A+ SKE GVEKF A T Y+
Sbjct: 140 AKKSKETGVEKFYEEYQRLASGIEVTLYL 168
>gnl|CDD|178429 PLN02835, PLN02835, oxidoreductase.
Length = 539
Score = 29.9 bits (67), Expect = 2.0
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 256 VVMKKGEPDYGYYRYDLRYDPVMPLK-----LFINGLFPG 290
V + GE Y YY + + Y + PL + ING FPG
Sbjct: 20 VSLVNGEDPYKYYTWTVTYGTISPLGVPQQVILINGQFPG 59
>gnl|CDD|187567 cd05257, Arna_like_SDR_e, Arna decarboxylase_like, extended (e)
SDRs. Decarboxylase domain of ArnA. ArnA, is an enzyme
involved in the modification of outer membrane protein
lipid A of gram-negative bacteria. It is a bifunctional
enzyme that catalyzes the NAD-dependent decarboxylation
of UDP-glucuronic acid and
N-10-formyltetrahydrofolate-dependent formylation of
UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent
decaboxylating activity is in the C-terminal 360
residues. This subgroup belongs to the extended SDR
family, however the NAD binding motif is not a perfect
match and the upstream Asn of the canonical active site
tetrad is not conserved. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 29.6 bits (67), Expect = 2.1
Identities = 17/84 (20%), Positives = 31/84 (36%), Gaps = 22/84 (26%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRND---- 78
V GA G++GS+L +L ++G ++VR L + +
Sbjct: 4 VTGADGFIGSHLTERLLREG-----------HEVRALDIYNSFNSWGLLDNAVHDRFHFI 52
Query: 79 -------DEIRKAIKYSNVVINLI 95
E+ +K +VV +L
Sbjct: 53 SGDVRDASEVEYLVKKCDVVFHLA 76
>gnl|CDD|184025 PRK13394, PRK13394, 3-hydroxybutyrate dehydrogenase; Provisional.
Length = 262
Score = 29.5 bits (66), Expect = 2.2
Identities = 19/101 (18%), Positives = 40/101 (39%), Gaps = 8/101 (7%)
Query: 14 SSFNGVVATVFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLG-QVLFQP 72
S+ NG A V GA+ +G + +L + G+ + I G + +
Sbjct: 3 SNLNGKTAVVTGAASGIGKEIALELARAGAAVAIADLNQDGANAVADEINKAGGKAIGVA 62
Query: 73 YHPRNDDEIRKAIKYSNVVINLIGREFATKNFTIADANVEI 113
N+D + N I+ + F + + +++A ++I
Sbjct: 63 MDVTNEDAV-------NAGIDKVAERFGSVDILVSNAGIQI 96
>gnl|CDD|187594 cd05333, BKR_SDR_c, beta-Keto acyl carrier protein reductase
(BKR), involved in Type II FAS, classical (c) SDRs.
This subgroup includes the Escherichai coli K12 BKR,
FabG. BKR catalyzes the NADPH-dependent reduction of
ACP in the first reductive step of de novo fatty acid
synthesis (FAS). FAS consists of four elongation steps,
which are repeated to extend the fatty acid chain
through the addition of two-carbo units from malonyl
acyl-carrier protein (ACP): condensation, reduction,
dehydration, and a final reduction. Type II FAS,
typical of plants and many bacteria, maintains these
activities on discrete polypeptides, while type I FAS
utilizes one or two multifunctional polypeptides. BKR
resembles enoyl reductase, which catalyzes the second
reduction step in FAS. SDRs are a functionally diverse
family of oxidoreductases that have a single domain
with structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) NAD(P)(H)
binding region and a structurally diverse C-terminal
region. Classical SDRs are typically about 250 residues
long, while extended SDRS are approximately 350
residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes have a 3-glycine N-terminal
NAD(P)(H) binding pattern: TGxxxGxG in classical SDRs.
Extended SDRs have additional elements in the
C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P) binding motif and an altered
active site motif (YXXXN). Fungal type type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P) binding motif and missing or
unusual active site residues. Reactions catalyzed
within the SDR family include isomerization,
decarboxylation, epimerization, C=N bond reduction,
dehydratase activity, dehalogenation, Enoyl-CoA
reduction, and carbonyl-alcohol oxidoreduction. A
critical catalytic Tyr residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering), is often found in a conserved YXXXK
pattern. In addition to the Tyr and Lys, there is often
an upstream Ser (Ser-138, 15-PGDH numbering) and/or an
Asn (Asn-107, 15-PGDH numbering) or additional Ser,
contributing to the active site. Substrates for these
enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is
a proton relay involving the conserved Tyr-151 and
Lys-155, and well as Asn-111 (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is
not generally found among SDRs.
Length = 240
Score = 28.7 bits (65), Expect = 3.0
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 20 VATVFGASGYMGSYLCNKLGKQGSQIIIPYRGN 52
VA V GAS +G + +L +G+++ + R
Sbjct: 2 VALVTGASRGIGRAIALRLAAEGAKVAVTDRSE 34
>gnl|CDD|220634 pfam10220, DUF2146, Uncharacterized conserved protein (DUF2146).
This is a family of proteins conserved from plants to
humans. In Dictyostelium it is annotated as Mss11p but
this could not be confirmed. Mss11p is required for the
activation of pseudo-hyphal and invasive growth by
Ste12p in yeast.
Length = 890
Score = 29.1 bits (65), Expect = 3.2
Identities = 15/62 (24%), Positives = 23/62 (37%), Gaps = 1/62 (1%)
Query: 53 FYDVRDLRLCGDLGQVLFQPYHPRNDDEIRKAIKYSNVVINLIGREFATKNFTIADANVE 112
FY + C L + F + P + D IR A +N + E A + + E
Sbjct: 519 FYQHIAFKCCVKLWRYQFPIFQPSSSD-IRAADFENNSLSAAKKMEQAEDELADEETDQE 577
Query: 113 IP 114
P
Sbjct: 578 QP 579
>gnl|CDD|187563 cd05253, UDP_GE_SDE_e, UDP glucuronic acid epimerase, extended
(e) SDRs. This subgroup contains UDP-D-glucuronic acid
4-epimerase, an extended SDR, which catalyzes the
conversion of UDP-alpha-D-glucuronic acid to
UDP-alpha-D-galacturonic acid. This group has the SDR's
canonical catalytic tetrad and the TGxxGxxG NAD-binding
motif of the extended SDRs. Extended SDRs are distinct
from classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 332
Score = 28.8 bits (65), Expect = 3.5
Identities = 12/36 (33%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQII-IPYRGNFYDVR 57
V GA+G++G ++ +L ++G +++ I ++YDVR
Sbjct: 5 VTGAAGFIGFHVAKRLLERGDEVVGIDNLNDYYDVR 40
>gnl|CDD|178587 PLN03013, PLN03013, cysteine synthase.
Length = 429
Score = 29.0 bits (64), Expect = 3.7
Identities = 10/50 (20%), Positives = 16/50 (32%), Gaps = 2/50 (4%)
Query: 217 GDVAAAIVAACKDPDAAGKIYQAVGPK--RYLLSELLDWFHVVMKKGEPD 264
G AAA + K P+ AGK+ R + + +
Sbjct: 379 GAAAAAAIKVAKRPENAGKLIAVSLFASGRDIYTPRCSSLSGKRWRKCSL 428
>gnl|CDD|177651 PLN00011, PLN00011, cysteine synthase.
Length = 323
Score = 28.4 bits (63), Expect = 4.9
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 217 GDVAAAIVAACKDPDAAGKIYQAVGP---KRYLLSELLD 252
G AAA + K P+ AGK+ + P +RYL ++L +
Sbjct: 273 GAAAAAALKVAKRPENAGKLIVVIFPSGGERYLSTKLFE 311
>gnl|CDD|166206 PLN02565, PLN02565, cysteine synthase.
Length = 322
Score = 28.0 bits (62), Expect = 5.9
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 217 GDVAAAIVAACKDPDAAGKIYQAVGP---KRYLLSELLD 252
G AAA + K P+ AGK+ + P +RYL S L +
Sbjct: 271 GAAAAAAIKIAKRPENAGKLIVVIFPSFGERYLSSVLFE 309
>gnl|CDD|217105 pfam02558, ApbA, Ketopantoate reductase PanE/ApbA. This is a
family of 2-dehydropantoate 2-reductases also known as
ketopantoate reductases, EC:1.1.1.169. The reaction
catalyzed by this enzyme is: (R)-pantoate + NADP(+) <=>
2-dehydropantoate + NADPH. AbpA catalyzes the NADPH
reduction of ketopantoic acid to pantoic acid in the
alternative pyrimidine biosynthetic (APB) pathway. ApbA
and PanE are allelic. ApbA, the ketopantoate reductase
enzyme is required for the synthesis of thiamine via the
APB biosynthetic pathway.
Length = 150
Score = 27.6 bits (62), Expect = 5.9
Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 13/91 (14%)
Query: 22 TVFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYD---VRDLRLCGDLGQVLFQPYHPRND 78
+ GA G +GS +L + G + + RG + LR+ G+ P P
Sbjct: 2 AILGA-GAVGSLYGARLARAGHDVTLIARGRHLEAIRENGLRITSPGGERTVPP--PVAT 58
Query: 79 DEIRKAIKYSNVVINLIGREFATKNFTIADA 109
+ V++ A K + A+A
Sbjct: 59 SASEELGPADLVIV-------AVKAYQTAEA 82
>gnl|CDD|145171 pfam01863, DUF45, Protein of unknown function DUF45. This protein
has no known function. Members are found in some
archaebacteria, as well as Helicobacter pylori. The
proteins are 190-240 amino acids long, with the C
terminus being the most conserved region, containing
three conserved histidines. This motif is similar to
that found in Zinc proteases, suggesting that this
family may also be proteases.
Length = 205
Score = 27.7 bits (62), Expect = 6.1
Identities = 17/85 (20%), Positives = 28/85 (32%), Gaps = 11/85 (12%)
Query: 43 SQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPRNDDEIRKAIKYSNVVINLIGREFATK 102
S P G Y RL G+ L + + + + + K
Sbjct: 55 SGESFPLLGKKY-----RLKVIPGKRLSVTLLRDGLELVVLVELDPEKLRKAL-ERWLRK 108
Query: 103 NFTIADANVEIPARLARLSKEMGVE 127
A E+ RLAR ++++GV
Sbjct: 109 R-----AKEELEERLARYAEKLGVR 128
>gnl|CDD|163279 TIGR03466, HpnA, hopanoid-associated sugar epimerase. The
sequences in this family are members of the pfam01370
superfamily of NAD-dependent epimerases and dehydratases
typically acting on nucleotide-sugar substrates. The
genes of the family modeled here are generally in the
same locus with genes involved in the biosynthesis and
elaboration of hopene, the cyclization product of the
polyisoprenoid squalene. This gene and its association
with hopene biosynthesis in Zymomonas mobilis has been
noted in the literature where the gene symbol hpnA was
assigned. Hopanoids are known to be components of the
plasma membrane and to have polar sugar head groups in
Z. mobilis and other species.
Length = 328
Score = 28.0 bits (63), Expect = 6.8
Identities = 47/183 (25%), Positives = 74/183 (40%), Gaps = 33/183 (18%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLR------LCGDLGQVLFQPYHPR 76
V GA+G++GS + L +QG ++ + R D R+L + GDL R
Sbjct: 5 VTGATGFVGSAVVRLLLEQGEEVRVLVRPT-SDRRNLEGLDVEIVEGDL----------R 53
Query: 77 NDDEIRKAIKYSNVVINLIG--REFATKNFTIADANVEIPARLARLSKEMGVEKFIHIS- 133
+ +RKA+ + ++ R +A + ANVE L R + E GVE+ ++ S
Sbjct: 54 DPASLRKAVAGCRALFHVAADYRLWAPDPEEMYAANVEGTRNLLRAALEAGVERVVYTSS 113
Query: 134 ----ALNADPNPP--TYYISGGS---QFYRTKYQGEKEVLREFPE----ATIFRPSDMYG 180
+ D P T S + R+K+ E+ L E I PS G
Sbjct: 114 VATLGVRGDGTPADETTPSSLDDMIGHYKRSKFLAEQAALEMAAEKGLPVVIVNPSTPIG 173
Query: 181 SGD 183
D
Sbjct: 174 PRD 176
>gnl|CDD|233557 TIGR01746, Thioester-redct, thioester reductase domain. This model
includes the terminal domain from the fungal alpha
aminoadipate reductase enzyme (also known as
aminoadipate semialdehyde dehydrogenase) which is
involved in the biosynthesis of lysine , as well as the
reductase-containing component of the myxochelin
biosynthetic gene cluster, MxcG. The mechanism of
reduction involves activation of the substrate by
adenylation and transfer to a covalently-linked
pantetheine cofactor as a thioester. This thioester is
then reduced to give an aldehyde (thus releasing the
product) and a regenerated pantetheine thiol. (In
myxochelin biosynthesis this aldehyde is further reduced
to an alcohol or converted to an amine by an
aminotransferase.) This is a fundamentally different
reaction than beta-ketoreductase domains of polyketide
synthases which act at a carbonyl two carbons removed
from the thioester and forms an alcohol as a product.
This domain is invariably found at the C-terminus of the
proteins which contain it (presumably because it results
in the release of the product). The majority of hits to
this model are non-ribosomal peptide synthetases in
which this domain is similarly located proximal to a
thiolation domain (pfam00550). In some cases this domain
is found at the end of a polyketide synthetase enzyme,
but is unlike ketoreductase domains which are found
before the thiolase domains. Exceptions to this observed
relationship with the thiolase domain include three
proteins which consist of stand-alone reductase domains
(GP|466833 from M. leprae, GP|435954 from Anabaena and
OMNI|NTL02SC1199 from Strep. coelicolor) and one protein
(OMNI|NTL01NS2636 from Nostoc) which contains N-terminal
homology with a small group of hypothetical proteins but
no evidence of a thiolation domain next to the putative
reductase domain. Below the noise cutoff to this model
are proteins containing more distantly related
ketoreductase and dehydratase/epimerase domains. It has
been suggested that a NADP-binding motif can be found in
the N-terminal portion of this domain that may form a
Rossman-type fold.
Length = 367
Score = 28.1 bits (63), Expect = 6.8
Identities = 58/284 (20%), Positives = 101/284 (35%), Gaps = 60/284 (21%)
Query: 22 TVF--GASGYMGSYLCNKLGKQGSQ--IIIPYRG--------------NFYDVRDLRL-- 61
TV GA+G++G+YL +L ++ +Q +I R Y + L
Sbjct: 1 TVLLTGATGFLGAYLLEELLRRSTQAKVICLVRAASEEHAMERLREALRSYRLWHEDLAR 60
Query: 62 ------CGDLGQVLFQPYHPRNDDEIRKAIKYSNVVINLIGREFATKNF-----TIADAN 110
GDL + PR + + + V + I A N+ + AN
Sbjct: 61 ERIEVVAGDLSE-------PRLGLSDAEWERLAENV-DTIVHNGALVNWVYPYSELRGAN 112
Query: 111 VEIPARLARLSKEMGVEKFIHISALNA-----------DPNPPTYYISGGSQFYRTKYQG 159
V + RL+ + ++S ++ D T + ++K+
Sbjct: 113 VLGTREVLRLAASGRAKPLHYVSTISVGAAIDLSTVTEDDATVTPPPGLAGGYAQSKWVA 172
Query: 160 EKEVLREFPE----ATIFRPSDMYGSGDKFLRYYGHMWRHVFR---KLAVYKKGEETIKQ 212
E ++RE + TI RP + G+ + + + L Y + E +
Sbjct: 173 EL-LVREASDRGLPVTIVRPGRILGNSYTGAINSSDILWRMVKGCLALGAYPQSPELTED 231
Query: 213 PVYVGDVAAAIV--AACKDPDAAGKIYQAVGPKRYLLSELLDWF 254
V VA AIV ++ A G ++ V P+ L E LDW
Sbjct: 232 LTPVDFVARAIVVLSSRPAASAGGPVFHVVNPEPVSLDEFLDWL 275
>gnl|CDD|233325 TIGR01238, D1pyr5carbox3, delta-1-pyrroline-5-carboxylate
dehydrogenase (PutA C-terminal domain). This model
represents one of several related branches of
delta-1-pyrroline-5-carboxylate dehydrogenase. Members
of this branch are the C-terminal domain of the PutA
bifunctional proline dehydrogenase /
delta-1-pyrroline-5-carboxylate dehydrogenase [Energy
metabolism, Amino acids and amines].
Length = 500
Score = 28.0 bits (62), Expect = 7.1
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 6/47 (12%)
Query: 185 FLRYYGHMWRHVFRKLAVYKKGEETIKQP------VYVGDVAAAIVA 225
F RYY R V + +V +G P ++ G ++AA+ A
Sbjct: 141 FCRYYAKQVRDVLGEFSVESRGVFVCISPWNFPLAIFTGQISAALAA 187
>gnl|CDD|235506 PRK05565, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 247
Score = 27.5 bits (62), Expect = 7.2
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 16 FNGVVATVFGASGYMGSYLCNKLGKQGSQIIIPYRGN 52
G VA V GASG +G + L K+G++++I Y N
Sbjct: 3 LMGKVAIVTGASGGIGRAIAELLAKEGAKVVIAYDIN 39
>gnl|CDD|219583 pfam07799, DUF1643, Protein of unknown function (DUF1643). The
members of this family are all sequences found within
hypothetical proteins expressed by various bacterial
species. The region concerned is approximately 150
residues long.
Length = 136
Score = 26.8 bits (60), Expect = 7.8
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 7/38 (18%)
Query: 55 DVRDLRLCGDLGQVLFQPYHPRNDDEIRKAIKYSNVVI 92
D +DLR D P P ND + +A K+++ V+
Sbjct: 61 DPKDLRRAAD-------PVGPENDAHLLRAAKWADDVV 91
>gnl|CDD|187671 cd09811, 3b-HSD_HSDB1_like_SDR_e, human 3beta-HSD (hydroxysteroid
dehydrogenase) and HSD3B1(delta 5-delta
4-isomerase)-like, extended (e) SDRs. This extended-SDR
subgroup includes human 3 beta-HSD/HSD3B1 and C(27)
3beta-HSD/ [3beta-hydroxy-delta(5)-C(27)-steroid
oxidoreductase; HSD3B7], and related proteins. These
proteins have the characteristic active site tetrad and
NAD(P)-binding motif of extended SDRs. 3 beta-HSD
catalyzes the oxidative conversion of delta 5-3
beta-hydroxysteroids to the delta 4-3-keto
configuration; this activity is essential for the
biosynthesis of all classes of hormonal steroids. C(27)
3beta-HSD is a membrane-bound enzyme of the endoplasmic
reticulum, it catalyzes the isomerization and oxidation
of 7alpha-hydroxylated sterol intermediates, an early
step in bile acid biosynthesis. Mutations in the human
gene encoding C(27) 3beta-HSD underlie a rare autosomal
recessive form of neonatal cholestasis. Extended SDRs
are distinct from classical SDRs. In addition to the
Rossmann fold (alpha/beta folding pattern with a central
beta-sheet) core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids. Extended SDRs are a
diverse collection of proteins, and include isomerases,
epimerases, oxidoreductases, and lyases; they typically
have a TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid sythase have
a GGXGXXG NAD(P)-binding motif and an altered active
site motif (YXXXN). Fungal type ketoacyl reductases have
a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 354
Score = 27.9 bits (62), Expect = 8.0
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 9/59 (15%)
Query: 174 RPSDMYGSGDKFLR-YYGHMWRH---VFRKLAVYKKGEETIKQPVYVGDVAAAIVAACK 228
RP +YG G FL + + + +F ++ + VYVG+VA A + A K
Sbjct: 183 RPMYIYGEGSHFLTEIFDFLLTNNGWLFPRIK-----GSGVNPLVYVGNVAWAHILAAK 236
>gnl|CDD|216106 pfam00762, Ferrochelatase, Ferrochelatase.
Length = 311
Score = 27.5 bits (62), Expect = 8.5
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 111 VEIPARLARLSKEMGVEKFIHISALNADP 139
E+ L++E G E + I LN P
Sbjct: 269 YELDIEYRELAEEAGGENYRRIPCLNDSP 297
>gnl|CDD|187541 cd05230, UGD_SDR_e, UDP-glucuronate decarboxylase (UGD) and
related proteins, extended (e) SDRs. UGD catalyzes the
formation of UDP-xylose from UDP-glucuronate; it is an
extended-SDR, and has the characteristic glycine-rich
NAD-binding pattern, TGXXGXXG, and active site tetrad.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving
as a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton
relay involving the conserved Tyr and Lys, a water
molecule stabilized by Asn, and nicotinamide. Atypical
SDRs generally lack the catalytic residues
characteristic of the SDRs, and their glycine-rich
NAD(P)-binding motif is often different from the forms
normally seen in classical or extended SDRs. Complex
(multidomain) SDRs such as ketoreductase domains of
fatty acid synthase have a GGXGXXG NAD(P)-binding motif
and an altered active site motif (YXXXN). Fungal type
ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding
motif.
Length = 305
Score = 27.6 bits (62), Expect = 8.7
Identities = 9/25 (36%), Positives = 19/25 (76%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIII 47
+ G +G++GS+LC++L + G ++I
Sbjct: 5 ITGGAGFLGSHLCDRLLEDGHEVIC 29
>gnl|CDD|215035 PLN00033, PLN00033, photosystem II stability/assembly factor;
Provisional.
Length = 398
Score = 27.5 bits (61), Expect = 9.8
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 7/54 (12%)
Query: 23 VFGASGYMGSYLCNKLGKQGSQIIIPYRGNFYDVRDLRLCGDLGQVLFQPYHPR 76
+ GAS Y G++ G + + RGNFY L + GQ +QP H R
Sbjct: 231 ISGASYYTGTFSTVNRSPDGDYVAVSSRGNFY------LTWEPGQPYWQP-HNR 277
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.142 0.438
Gapped
Lambda K H
0.267 0.0800 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,511,555
Number of extensions: 1640035
Number of successful extensions: 1862
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1807
Number of HSP's successfully gapped: 82
Length of query: 303
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 207
Effective length of database: 6,679,618
Effective search space: 1382680926
Effective search space used: 1382680926
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.4 bits)